Merge branch 'master' into drdx

README.md

@@ -5,10 +5,12 @@
 
 ## Code Description
 - Code uses deal.II library as the backbone (https://www.dealii.org/)
-- Supported Partial Differential Equations: Convection-diffusion, Euler, TODO: Navier-Stokes.
-- Supported convective numerical fluxes: Lax-Friedrichs, Roe (Harten's entropy fix) for Euler
+- Math supporting this code can be viewed in this **very rough draft in progress** [Overleaf document](https://www.overleaf.com/read/mytvbbbbyqnj).
+- Supports weak and strong (InProgress) form of discontinuous Galerkin (DG), and flux reconstruction (FR) (InProgress)
+- Supported Partial Differential Equations: Linear advection, diffusion, convection-diffusion, Burgers, Euler, TODO: Navier-Stokes.
+- Supported convective numerical fluxes: Lax-Friedrichs, Roe (Harten's entropy fix) for Euler, InProgress: Split-Form
 - Supported diffusive numerical fluxes: Symmetric Interior Penalty
-- Supported elements: LINEs, QUADs, HEXs
+- Supported elements: LINEs, QUADs, HEXs since it uses deal.II
 - Supported refinements: h (size) or p (order).
 
 ## Building/Running the Code
@@ -68,6 +70,7 @@ ROOT$ ctest -R <regex> (Run tests matching regular expression)
 ROOT$ ctest -E <regex> (Exclude tests matching regular expression)
 ROOT$ ctest -V (Enable verbose output from tests)
 ```
+Note that running `ctest` in `Debug` will take forever since some integration tests fully solve nonlinear problems with multiple orders and multiple meshes. It is suggested to perform `ctest` in `Release` mode, and only use `Debug` mode for debugging purposes.
 
 ## Debugging
 
@@ -95,11 +98,11 @@ GDB$ quit
 
 ### Parallel debugging
 
-If the error only occurs when using parallelism, you can use the following
-
+If the error only occurs when using parallelism, you can use the following example command
 ```sh
-mpirun -np 2 xterm -hold -e gdb -ex 'break MPI_Abort' -ex run --args /home/ddong/Codes/PHiLiP_temp/PHiLiP/build_debug/bin/PHiLiP_2D "-i" "/home/ddong/Codes/PHiLiP_temp/PHiLiP/build_de    bug/tests/advection_implicit/2d_advection_implicit_strong.prm"
+mpirun -np 2 xterm -hold -e gdb -ex 'break MPI_Abort' -ex run --args /home/ddong/Codes/PHiLiP_temp/PHiLiP/build_debug/bin/PHiLiP_2D "-i" "/home/ddong/Codes/PHiLiP_temp/PHiLiP/build_debug/tests/advection_implicit/2d_advection_implicit_strong.prm"
 ```
+This launches 2 xterm processes, each of which will launch gdb processes that will run the code and will have a breakpoint when MPI_Abort is encountered.
 
 
 # License

src/dg/dg.cpp

@@ -148,6 +148,66 @@ DGBase<dim,real>::create_collection_tuple(const unsigned int max_degree, const i
     dealii::hp::QCollection<1>         oned_quad_coll;
 
     dealii::hp::FECollection<dim>      fe_coll_lagr;
+
+    // for p=0, we use a p=1 FE for collocation, since there's no p=0 quadrature for Gauss Lobatto
+    if (parameters_input->use_collocated_nodes==true)
+    {
+    	int degree = 1;
+		//const dealii::MappingQ<dim,dim> mapping(degree, true);
+		//const dealii::MappingQ<dim,dim> mapping(degree+1, true);
+		//const dealii::MappingManifold<dim,dim> mapping;
+		//mapping_coll.push_back(mapping);
+
+		const dealii::FE_DGQ<dim> fe_dg(degree);
+		const dealii::FESystem<dim,dim> fe_system(fe_dg, nstate);
+		fe_coll.push_back (fe_system);
+
+		//
+
+		dealii::Quadrature<1>     oned_quad(degree+1);
+		dealii::Quadrature<dim>   volume_quad(degree+1);
+		dealii::Quadrature<dim-1> face_quad(degree+1); //removed const
+
+		if (parameters_input->use_collocated_nodes)
+			{
+				dealii::QGaussLobatto<1> oned_quad_Gauss_Lobatto (degree+1);
+				dealii::QGaussLobatto<dim> vol_quad_Gauss_Lobatto (degree+1);
+				oned_quad = oned_quad_Gauss_Lobatto;
+				volume_quad = vol_quad_Gauss_Lobatto;
+
+				if(dim == 1)
+				{
+					dealii::QGauss<dim-1> face_quad_Gauss_Legendre (degree+1);
+					face_quad = face_quad_Gauss_Legendre;
+				}
+				else
+				{
+					dealii::QGaussLobatto<dim-1> face_quad_Gauss_Lobatto (degree+1);
+					face_quad = face_quad_Gauss_Lobatto;
+				}
+
+
+			}
+			else
+			{
+				dealii::QGauss<1> oned_quad_Gauss_Legendre (degree+1);
+				dealii::QGauss<dim> vol_quad_Gauss_Legendre (degree+1);
+				dealii::QGauss<dim-1> face_quad_Gauss_Legendre (degree+1);
+				oned_quad = oned_quad_Gauss_Legendre;
+				volume_quad = vol_quad_Gauss_Legendre;
+				face_quad = face_quad_Gauss_Legendre;
+			}
+		//
+
+
+		volume_quad_coll.push_back (volume_quad);
+		face_quad_coll.push_back (face_quad);
+		oned_quad_coll.push_back (oned_quad);
+
+		dealii::FE_DGQArbitraryNodes<dim,dim> lagrange_poly(oned_quad);
+		fe_coll_lagr.push_back (lagrange_poly);
+    }
+
     int minimum_degree = (parameters_input->use_collocated_nodes==true) ?  1 :  0;
     for (unsigned int degree=minimum_degree; degree<=max_degree; ++degree) {
         //const dealii::MappingQ<dim,dim> mapping(degree, true);

src/parameters/all_parameters.cpp

@@ -47,7 +47,9 @@ void AllParameters::declare_parameters (dealii::ParameterHandler &prm)
                       " euler_vortex | "
                       " euler_entropy_waves | "
                       " numerical_flux_convervation | "
-                      " jacobian_regression "),
+                      " jacobian_regression |"
+                      " advection_periodicity |"
+                      " euler_split_taylor_green"),
                       "The type of test we want to solve. "
                       "Choices are (only run control has been coded up for now)" 
                       " <run_control | " 
@@ -57,7 +59,9 @@ void AllParameters::declare_parameters (dealii::ParameterHandler &prm)
                       "  euler_vortex | "
                       "  euler_entropy_waves | "
                       "  numerical_flux_convervation | "
-                      "  jacobian_regression>.");
+                      "  jacobian_regression |"
+					  "  euler_split_taylor_green |"
+					  "  advection_periodicity >.");
 
     prm.declare_entry("pde_type", "advection",
                       dealii::Patterns::Selection(
@@ -111,6 +115,8 @@ void AllParameters::parse_parameters (dealii::ParameterHandler &prm)
     else if (test_string == "euler_entropy_waves") { test_type = euler_entropy_waves; }
     else if (test_string == "numerical_flux_convervation") { test_type = numerical_flux_convervation; }
     else if (test_string == "jacobian_regression") { test_type = jacobian_regression; }
+    else if (test_string == "advection_periodicity") {test_type = advection_periodicity; }
+    else if (test_string == "euler_split_taylor_green") {test_type = euler_split_taylor_green;}
 
     const std::string pde_string = prm.get("pde_type");
     if (pde_string == "advection") {

src/physics/CMakeLists.txt

@@ -5,7 +5,7 @@ SET(SOURCE
     burgers.cpp
     euler.cpp
     manufactured_solution.cpp
-    # mhd.cpp
+    mhd.cpp
     )
 
 foreach(dim RANGE 1 3)